panX no working
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0
Entering edit mode
4 weeks ago

Hello, I am trying to use panX for my pangenome analysis. After installing all the dependencies, when I run the test.sh, I am getting the following error.

sh run-TestSet.sh
cat: '/home/saiful/pan-genome-analysis/data/TestSet/protein_faa/*faa': No such file or directory
Traceback (most recent call last):
  File "./panX.py", line 277, in <module>
    myPangenome.clustering_protein_sequences()
  File "/home/saiful/pan-genome-analysis/scripts/pangenome_computation.py", line 139, in clustering_protein_sequences
    self.diamond_identity, self.diamond_query_cover, self.diamond_subject_cover, self.diamond_path, self.mcl_inflation)
  File "/home/saiful/pan-genome-analysis/scripts/sf_cluster_protein.py", line 232, in clustering_protein
    return parse_geneCluster(cluster_fpath, cluster_dt_cpk_fpath)
  File "/home/saiful/pan-genome-analysis/scripts/sf_cluster_protein.py", line 126, in parse_geneCluster
    with open(input_fpath, 'rb') as infile:
IOError: [Errno 2] No such file or directory: '/home/saiful/pan-genome-analysis/data/TestSet/protein_faa/diamond_matches/allclusters.tsv'

Where is the problem?Can anyone suggest me? Is there any better tools for pangenome analysis?

Thank you

panX error • 184 views
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Entering edit mode

Looks like you are missing directory/files as indicated. How did you install? With conda?

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yes. I have installed it with conda. Is it making any problem?

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